"The number of cases is decreasing week by week and getting to zero in many places... But we still see occasional flare-ups and we still see some surprises with new cases out of our contact lists," Nabarro told AFP.
"That means that the epidemic is not contained yet," he said.
Nabarro was speaking at the African Union headquarters, as leaders gather a day ahead of a summit meeting where Ebola is a key issue for discussion.
The three nations have been devastated by the outbreak, which began in December 2013, but all have seen recent signs that the virus is on the wane, with the number of new cases dropping weekly.
Liberia, once the country worst hit by the outbreak, hopes to have no new cases by the end of next month.
"We must maintain the effort with even greater intensity, the forthcoming rainy season is a concern," Nabarro said.
"I took us too long to be ready, we need a better response capacity," he said. "The African CDC will allow the AU to be much quicker."
On Friday and Saturday African leaders are set to discuss the economic recovery of countries affected by Ebola, as well as the setting up a "solidarity fund" and planning the CDC centre, which in its initial phase would operate as an "early warning system".
Oxfam has called for a "massive post-Ebola Marshall Plan" for affected west African nations, referring to the United States aid package to rebuild Europe after World War II.
"It's clear that Africa's existing architecture for early disease detection, response and control is wholly inadequate," Oxfam said in a statement yesterday.
The World Health Organization admitted earlier this month that the UN agency had been caught napping on Ebola and pledged reforms to avoid similar mistakes in future.
